Re: CCL:Van Der Waals Collapse
|> From: Hodgkin, Ed
|> It is well known that molecular mechanics force fields favour 'folded'
|> conformations which derive stability from large Van Der Waals terms.
|> One could coin the phrase "Van Der Waals Collapse" to describe
From the earliest days of charmm development, this has been a concern.
Globular proteins simulated in vacuo shrink when "true" atomic radii
are used as the basis for nonbonded interaction parameters.
Swaminathan spent alot of time working on a compensating force term,
but I don't know what became of the work. The most direct way to
control for the self-association of peptide chains is to do a
simulation that includes solvation explicitly. Note that if you do
this as a water droplet rather than a periodic box the internal
pressure generated by surface tension is enormous so the system will
still collapse some compared to physiologic conditions.